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Article: Non-canonical base pairing

= Non-canonical base pairing = Non-canonical base pairing refers to instances in which nucleobases hydrogen bond, or base pair, to one another in schemes other than the Watson-Crick base pairs (adenine-thymine in DNA, adenine-uracil in RNA, and guanine-cytosine in both DNA and RNA).

History
James Watson and Francis Crick published the double helical structure of DNA and proposed the canonical Watson-Crick base pairs in 1953. Ten years later, in 1963, Karst Hoogsteen reported that he had used single crystal X-ray diffraction to investigate alternative base pair structures, and he found an alternative structure for the nucelobase pair adenine-thymine in which the purine (adenine) takes on an alternative conformation with respect to the pyrimidine (thymine). The adenine is rotated 180° about the glycosidic bond, resulting in an alternative hydrogen bonding scheme which has one hydrogen bond in common with the Watson-Crick base pair (adenine N6 and thymine N4), while the other, instead of occurring between adenine N1 and thymine N3 as in the Watson-Crick base pair, occurs between adenine N7 and thymine N3. Five years after Hoogsteen proposed the A-T Hoogsteen base pair, optical rotary dispersion spectra which provided evidence for a G-C Hoogsteen base pair were observed. Similarly to the A-T Hoogsteen base pair, the purine (guanine) is rotated 180° about the glycosidic bond while the pyrimidine (cytosine) remains in place. One hydrogen bond from the Watson-Crick base pair is maintained (guanine O6 and cytosine N4) and the other occurs between guanine N7 and a protonated cytosine N3 (note that the Hoogsteen G-C base pair has two hydrogen bonds, while the Watson-Crick G-C base pair has three). The G-C Hoogsteen base pair was first observed via X-ray crystallography years later, in 1986, by co-crystallizing DNA with triostin A (an antibiotic). Ultimately, after years of studying both Watson-Crick and Hoogsteen base pairs, it has been determined that both occur naturally in DNA, and that they exist in equilibrium with one another; the conditions in which the DNA exists ultimately determine which form will be favored.

Since the structures of the canonical Watson-Crick and non-canonical Hoogsteen base pairs were determined, many other types of non-canonical base pairs have been presented and described. Types of non-canonical base pairs can be defined by which faces of the nucleobases are interacting in a given base pair. When classified this way, nearly 40 types of non-canonical base pairs can be identified. These can be sorted into the larger categories of cis and trans.